sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.650 Å
X-ray
2011-06-09
| Name: | Proteasome subunit beta type-5 | Proteasome subunit beta type-6 |
|---|---|---|
| ID: | PSB5_YEAST | PSB6_YEAST |
| AC: | P30656 | P23724 |
| Organism: | Saccharomyces cerevisiae | |
| Reign: | Eukaryota | |
| TaxID: | 559292 | |
| EC Number: | 3.4.25.1 | |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| Y | 63 % |
| Z | 37 % |
| B-Factor: | 35.499 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.235 | 1171.125 |
| % Hydrophobic | % Polar |
|---|---|
| 46.97 | 53.03 |
| According to VolSite | |
| HET Code: | 3SD |
|---|---|
| Formula: | C32H41N5O5 |
| Molecular weight: | 575.698 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.7 % |
| Polar Surface area: | 142.43 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| 58.4911 | -157.562 | 15.8881 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C40 | CB | ALA- 20 | 4.26 | 0 | Hydrophobic |
| C26 | CB | ALA- 20 | 3.64 | 0 | Hydrophobic |
| N13 | O | THR- 21 | 2.73 | 156.1 | H-Bond (Ligand Donor) |
| O19 | N | THR- 21 | 2.95 | 149.38 | H-Bond (Protein Donor) |
| C40 | CB | ALA- 27 | 4.29 | 0 | Hydrophobic |
| C40 | CB | SER- 28 | 3.62 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 31 | 3.93 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 31 | 3.47 | 0 | Hydrophobic |
| C21 | CD | LYS- 33 | 4.25 | 0 | Hydrophobic |
| C23 | CG | LYS- 33 | 3.8 | 0 | Hydrophobic |
| C27 | SD | MET- 45 | 4.09 | 0 | Hydrophobic |
| C23 | CB | MET- 45 | 3.82 | 0 | Hydrophobic |
| N16 | O | GLY- 47 | 2.76 | 167.88 | H-Bond (Ligand Donor) |
| C9 | CB | ALA- 49 | 3.72 | 0 | Hydrophobic |
| C26 | CB | ALA- 49 | 3.56 | 0 | Hydrophobic |
| C25 | CB | ALA- 49 | 3.44 | 0 | Hydrophobic |
| O11 | N | ALA- 49 | 3 | 166.3 | H-Bond (Protein Donor) |
| C30 | CB | SER- 96 | 3.76 | 0 | Hydrophobic |
| C38 | CB | SER- 112 | 4.26 | 0 | Hydrophobic |
| N7 | OD1 | ASP- 114 | 3.11 | 151.34 | H-Bond (Ligand Donor) |
| C9 | CB | ASP- 114 | 4.13 | 0 | Hydrophobic |
| C6 | CG | PRO- 115 | 4.1 | 0 | Hydrophobic |
| N34 | OG | SER- 118 | 3.35 | 161.02 | H-Bond (Ligand Donor) |
| C39 | CB | GLU- 120 | 4.27 | 0 | Hydrophobic |
